Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well

We present genome sequences of three Pseudomonadota strains isolated from an abandoned century-old oil exploration well. A Pseudomonas sp. genome showed a size of 5,378,420 bp, while Acinetobacter genomes sized 3,522,593 and 3,864,311 bp. Genomes included catabolic genes for benzoate, 4-hydroxybenzoate, salicylate, vanillate, indoleacetate, anthranilate, n-alkanes, 4-hydroxyphenylacetate, phenylacetate, among others

Occurrence and diffusive air-seawater exchanges of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in Fildes Bay, King George Island, Antarctica

We report the levels of organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in seawater and air, and the air-sea dynamics through diffusive exchange analysis in Fildes Bay, King George Island, Antarctica, between November 2019 and January 30, 2020. Hexachlorobenzene (HCB) was the most abundant compound in both air and seawater with concentrations around 39 ± 2.1 pg m−3 and 3.2 ± 2.4 pg L−1 respectively. The most abundant PCB congener was PCB 11, with a mean of 3.16 ± 3.7 pg m−3 in air and 2.0 ± 1.1 pg L−1 in seawater. The fugacity gradient estimated for the OCP compounds indicate a predominance of net atmospheric deposition for HCB, α-HCH, γ-HCH, 4,4′-DDT, 4,4′-DDE and close to equilibrium for the PeCB compound. The observed deposition of some OCs may be driven by high biodegradation rates and/or settling fluxes decreasing the concentration of these compounds in surface waters, which is supported by the capacity of microbial consortium to degrade some of these compounds. The estimated fugacity gradients for PCBs showed differences between congeners, with net volatilization predominating for PCB-9, a trend close to equilibrium for PCB congeners 11, 28, 52, 101, 118, 138, and 153, and deposition for PCB 180. Snow amplification may play an important role for less hydrophobic PCBs, with volatilization predominating after snow/glacier melting. As hydrophobicity increases, the biological pump decreases the concentration of PCBs in seawater, reversing the fugacity gradient to atmospheric deposition. This study highlights the potential impacts of climate change, through glacier retreat, on the biogeochemistry of POPs, remobilizing those compounds previously trapped within the cryosphere which in turn will transform the Antarctic cryosphere into a secondary source of the more volatile POPs in coastal areas, influenced by snow and ice melting

Predatory Activity of Myxobacteria Corallococcus exiguus against Soil Inhabiting Bacteria

Prokaryotic micropredators, including myxobacteria, shape the structure of the community in the soil as they prey on other microorganisms. Their unique behavior in nature has raised the interest in exploiting these bacterial groups to combat the threatening antibiotic resistance. The objective of this study is to assay the antibacterial activity of Corallococcus exiguus, a member of myxobacteria, based on their predation ability against soil inhabiting bacteria. A total of 17 soil bacteria from different taxa were preyed upon three C. exiguus isolates on TPM buffer agar medium. Based on the predation assay, all the three isolates actively killed all the Gram-negative Alphaproteobacteria and Betaproteobacteria members used in this study. Protease producing assay using casein as substrate revealed that these isolates were able to break down the protein with lytic index up to 1.33 ± 0.10. Their ethyl acetate extracts slightly inhibited the growth of one selected Gram-positive bacterium. Hydrolytic enzyme and secondary metabolite produced by C. exiguus are considered to play an important role in their predation activity.

Predatory Activity of Myxobacteria Corallococcus exiguus against Soil Inhabiting Bacteria

Prokaryotic micropredators, including myxobacteria, shape the structure of the community in the soil as they prey on other microorganisms. Their unique behavior in nature has raised the interest in exploiting these bacterial groups to combat the threatening antibiotic resistance. The objective of this study is to assay the antibacterial activity of Corallococcus exiguus, a member of myxobacteria, based on their predation ability against soil inhabiting bacteria. A total of 17 soil bacteria from different taxa were preyed upon three C. exiguus isolates on TPM buffer agar medium. Based on the predation assay, all the three isolates actively killed all the Gram-negative Alphaproteobacteria and Betaproteobacteria members used in this study. Protease producing assay using casein as substrate revealed that these isolates were able to break down the protein with lytic index up to 1.33 ± 0.10. Their ethyl acetate extracts slightly inhibited the growth of one selected Gram-positive bacterium. Hydrolytic enzyme and secondary metabolite produced by C. exiguus are considered to play an important role in their predation activity.

Shotgun metagenomes from productive lakes in an urban region of Sweden

Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Malaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Malaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes

Composition of the Metabolomic Bio-Coronas Isolated from \u3cem\u3eOcimum sanctum\u3c/em\u3e and \u3cem\u3eRubia tinctorum\u3c/em\u3e

Objective: Nanoharvesting from intact plants, organs, and cultured cells is a method in which nanoparticles are co-incubated with the target tissue, which leads to the internalization of nanoparticles. Internalized nanoparticles are coated in situ with specific metabolites that form a dynamic surface layer called a bio-corona. Our previous study showed that metabolites that form the bio-corona around anatase TiO2 nanoparticles incubated with leaves of the model plant Arabidopsis thaliana are enriched for flavonoids and lipids. The present study focused on the identification of metabolites isolated by nanoharvesting from two medicinal plants, Ocimum sanctum (Tulsi) and Rubia tinctorum (common madder). Results: To identify metabolites that form the bio-corona, Tulsi leaves and madder roots were incubated with ultra-small anatase TiO2 nanoparticles, the coated nanoparticles were collected, and the adsorbed molecules were released from the nanoparticle surface and analyzed using an untargeted metabolomics approach. Similar to the results in which Arabidopsis tissue was used as a source of metabolites, TiO2 nanoparticle bio-coronas from Tulsi and madder were enriched for flavonoids and lipids, suggesting that nanoharvesting has a wide-range application potential. The third group of metabolites enriched in bio-coronas isolated from both plants were small peptides with C-terminal arginine and lysine residues

Operationalizing Healthcare Big Data in the Electronic Health Records using a Heatmap Visualization Technique

Background: The majority of the electronic health record (EHR) contains a wealth of information, including unstructured notes. Healthcare professionals may be missing substantial portions of essential diagnostic and treatment information by not focusing on unstructured texts. The objective of this study is to present progress notes data using heatmap visualization. Methods: In this study, the research team used the unstructured text from the progress notes of deidentified patient data. The research team conducted qualitative content-coding based on the clinical complexity model and developed a heatmap based on the processed frequency data. Result: The researchers developed a color-coded heatmap focusing on the severity and acuity of patients’ status accumulated through multiple previous patient’s visits. Conclusions: Future research into creating an automated process to generate the heatmap from an unstructured dataset can open up opportunities to operationalize big data in healthcare

Optical mapping compendium of structural variants across global cattle breeds

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution

c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells

The transcription factor c-Maf induces the anti-inflammatory cytokine IL-10 in CD4+ T cells in vitro. However, the global effects of c-Maf on diverse immune responses in vivo are unknown. Here we found that c-Maf regulated IL-10 production in CD4+ T cells in disease models involving the TH1 subset of helper T cells (malaria), TH2 cells (allergy) and TH17 cells (autoimmunity) in vivo. Although mice with c-Maf deficiency targeted to T cells showed greater pathology in TH1 and TH2 responses, TH17 cell–mediated pathology was reduced in this context, with an accompanying decrease in TH17 cells and increase in Foxp3+ regulatory T cells. Bivariate genomic footprinting elucidated the c-Maf transcription-factor network, including enhanced activity of NFAT; this led to the identification and validation of c-Maf as a negative regulator of IL-2. The decreased expression of the gene encoding the transcription factor RORγt (Rorc) that resulted from c-Maf deficiency was dependent on IL-2, which explained the in vivo observations. Thus, c-Maf is a positive and negative regulator of the expression of cytokine-encoding genes, with context-specific effects that allow each immune response to occur in a controlled yet effective manner